Background: Bacteremia by Streptococcus pneumoniae has been traditionally associated with poor outcomes in patients with pneumonia; however, data on its impact on outcomes are limited and are sometimes contradictory. Methods: We performed a prospective study in two hospitals in northern Spain in which cases diagnosed with pneumococcal pneumonia were selected from a cohort of hospitalized patients with pneumonia between January 2001 and July 2009. We compared patients with pneumococcal bacteremic pneumonia with those with pneumococcal non-bacteremic pneumonia. Results: We compared 492 patients with negative blood culture and 399 with positive culture results. Host related factors were very similar in both groups. Severity of illness on admission measured by CURB-65 score was similar in both groups. Adjusted analysis showed a greater likelihood of septic shock during in-hospital course among patients with pneumococcal bacteremia (OR, 2.1; 95% CI, 1.2–3.5; P = 0.006). Likewise, patients with positive blood culture had greater in-hospital mortality (OR 2.1; 95% CI, 1.1 - -3.9; P = 0.02), 15-day mortality (OR 3.6; 95% CI, 1.7 - 7.4; P = 0.0006), and 30-day mortality (OR, 2.7; 95% CI, 1.5 - 5; P = 0.002). Conclusions: Although host related factors and severity on admission were very similar in the two groups, bacteremic patients had worse in-hospital course and outcomes. Bacteraemia in pneumococcal pneumonia is of prognostic significance.